Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny?

Abstract

The study of genomic organization and regulatory elements of rRNA genes in metazoan paradigmatic organisms has led to the most accepted model of rRNA gene organization in eukaryotes. Nevertheless, the rRNA genes of microbial eukaryotes have also been studied in considerable detail and their atypical structures have been considered as exceptions. However, it is likely that these organisms have preserved variations in the organization of a versatile gene that may be seen as living records of evolution. Here, we review the organization of the main rRNA transcription unit (rDNA) and the 5S rRNA genes (5S rDNA). These genes are reiterated in the genome of microbial eukaryotes and may be coded alone, in tandem repeats, linked to each other or linked to other genes. They may be found in the chromosome or extrachromosomally in linear or circular units. rDNA coding regions may contain introns, sequence insertions, protein-coding genes or additional spacers. The 5S rDNA can be found in tandem repeats or genetically linked to genes transcribed by RNA polymerases I, II or III. Available information from about a hundred microbial eukaryotes was used to review the unexpected diversity in the genomic organization of rRNA genes.

Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches

“…However, one of the drawbacks of the DGGE technique is the fact that the number of rRNA genes per chromosome equivalent differs widely in bacteria (27). In addition, heterogeneous copies of rRNA gene operons exist for both bacteria (37) and fungi (49), so that different bands may belong to the same species.…”

Trichomonas vaginalis ribosomal RNA: Identification and characterisation of the transcription promoter and terminator sequences

“…The rDNA regulatory elements are generally located within this region and include the TSP, the upstream control element (UCE), the promoter, enhancer regions, intergenic promoters and the transcription terminator. In most organisms, the ribosomal genes are grouped in tandem, and T. vaginalis has approximately 14 copies of this gene cluster [1]. Using genome sequencing data [18], we compared the larger rDNA contigs and found that the different copies of the rDNA sequence were almost identical.…”

“…Among protozoan organisms, there is enormous diversity in sequence and gene arrangement. Each transcriptional unit is separated by intergenic sequences that vary in length among organisms, ranging from 2 to 30 kbp [1]. Both the promoter and terminator sequences are located within this intergenic region.…”

Development of primers and a procedure for specific identification of the diatom Thalassiosira weissflogii

“…Sequence variations of internal transcribed spacers (ITS1 and ITS2) of 35S rDNA have been variously used as a molecular tool for species identification in eukaryotic organisms (Marinucci et al 1999;Wilkerson et al 2004;Torres-Machorro et al 2009). We designed a pair of conserved primers (18SF and 28SR1) from rDNA sequences of 22 diatom species reported in the GenBank database (see below).…”